EPIC-CoGe has a variety of pipelines for processing FastQ data. Its [[Expression Analysis Pipeline]] will clean your reads, map them, quantify their abundance to position in the genome, and quantify their abundance per transcript as FPKM values.

EPIC-CoGe has a variety of pipelines for processing FastQ data. Its [[Expression Analysis Pipeline]] will clean your reads, map them, quantify their abundance to position in the genome, and quantify their abundance per transcript as FPKM values.

* '''Note:''' You can add private experimental data to public genomes (Mix and match public and private data)

* '''Note:''' You can add private experimental data to public genomes (Mix and match public and private data)

When the load is finished, pressing "Genome View" will launch the genome viewer (JBrowse).

Note: The length of time it takes to load annotations depends on the load on the database and the number of annotations being loaded. For this example (and no load on the server), it should take ~ 3-5 minutes.

When the load is finished, pressing "Genome View" will launch the genome viewer (JBrowse).

Note: The length of time it takes to load annotations depends on the load on the database and the number of annotations being loaded. For this example (and no load on the server), it should take ~ 10-20 minutes.

When finished, you can get detailed information on the experiment (and modify what you've entered) in ExperimentView

From ExperimentView, you can launch the genome browser by pressing "View"

RNASeq Processing

EPIC-CoGe has a variety of pipelines for processing FastQ data. Its Expression Analysis Pipeline will clean your reads, map them, quantify their abundance to position in the genome, and quantify their abundance per transcript as FPKM values.

Note: You can add private experimental data to public genomes (Mix and match public and private data)